Methods for assessing whole genomes have become ever more important not only in research of genomes, but also in view of methods that aim at whole-genome manipulation to improve conditions, such as diseases. The methods for manipulating whole genomes by silencing a gene, inserting a new gene and editing or correcting genes are gaining significant importance.
However, to ensure that the methods aimed at improving the genome do not harm it, one must be aware of how the tools, such as double stranded DNA break causing agents, including enzymes, affect the genomes to be manipulated.
Methods for such large scale analysis have been lacking in the field of genomic analyses.
Mechanistic factors that influence translocations include DSB frequency at translocating loci and factors that influence such DSBs (Robbiani et al., 2008; Wang et al., 2009), factors that contribute to two translocating loci lying in close enough proximity in the interphase nucleus to be joined (Meaburn et al., 2007; Wang et al., 2009), and mechanisms that circumvent functions of the cellular DSB response and repair pathways that promote joining of DSBs within a chromosome and suppress joining of DSBs between chromosomes (Franco et al., 2006b; Ramiro et al., 2006).
For example, the mammalian nucleus is occupied by non-randomly positioned genes and chromosomes (Meaburn et al., 2007). DNA double-strand breaks (DSBs) fuse to generate translocations which requires physical proximity; thus, spatial disposition of chromosomes might impact translocation patterns. Cytogenetic studies have revealed that certain loci involved in oncogenic translocations are spatially proximal (Meaburn et al., 2007; Misteli and Soutoglou, 2009). Studies of recurrent translocations in mouse B cell lymphomas suggested that aspects of particular chromosomal regions, as opposed to broader territories, might promote spatial proximity and influence translocation frequency (Wang et al., 2009). Non-random position of genes and chromosomes in the nucleus led to two general models for translocation initiation. “Contact-first” poses translocations are restricted to proximally-positioned chromosomal regions; while “breakage-first” poses that distant DSBs can be juxtaposed (Meaburn et al., 2007).
In depth evaluation of how chromosomal organization influences translocations requires a genome-wide approach. Such genome-wide approaches could also be applied in evaluating agents that create DSBs for their cutting specificity and genome wide effects for recombination events throughout any given genome.